[BioC] GOstats

[Al Ivens]

Hi Francois,

Thanks for the prompt response.  I thought it might be a versioning
issue, but I religiously update every Monday AM!

I use:
* Windows GUI Menu
* Melbourne CRAN mirror
* all 4 repositories.

then run update packages from the menu.   This should do the trick,
shouldn't it, normally?  


The Biobase version was to make affyPLM and affyIO work with the latest
version of RMAExpress.  I shall
source("http://www.bioconductor.org/biocLite.R") as you suggest.

One other quick question: once one has done a:

require(mylibraryname)

is there a way of unloading it from RAM, so that an update can be done
without restarting the session?

Many thanks,

a


> -----Original Message-----
> From: Francois Pepin [mailto:fpepin at cs.mcgill.ca] 
> Sent: 12 September 2006 23:08
> To: Al Ivens
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] GOstats
> 
> 
> Hi Al,
> 
> GOstats depends on the GO package, which is updated at the 
> same time as the other annotation packages. That happens once 
> per stable release if I'm not mistaken.
> 
> My suggestion would be to update your annotations (e.g. KEGG, 
> hgu95av2 and GO) because they're quite out of date: versions 
> 1.6.5. The current version for bioC 1.8 is 1.12.0.
> 
> Running your query on an up-to-date version of the GO 
> annotation gives me the following:
> > GOTERM$"GO:0031975"@Term
> [1] "envelope"
> 
> I think you have a mix from different versions, because your 
> Biobase is version 1.11.17, while the current version for 
> bioC 1.8 is version 1.10.1. Sometimes strange behavior can 
> happen when packages from different versions are installed.
> 
> You can update your annotations using the biocLite 
> source("http://www.bioconductor.org/biocLite.R")
> and then updating the package that you want:
> biocLite('GO')
> 
> I strongly suggest that you update all of your annotation 
> packages to the same version, because code generally breaks 
> when your chip annotation, for example, points to a KEGG 
> pathway that the KEGG annotation ignores.
> 
> Hope this helps,
> 
> Francois
> 
> On Tue, 2006-09-12 at 22:43 +0100, Al Ivens wrote: 
> > Hi,
> > 
> > I am trying to use GOstats (1.6.0) for GOSlim analyses, but 
> have just 
> > realised that several of my selected Slim terms (chosen via AmiGO
> > http://www.godatabase.org/) are not in GOstats.
> > 
> > > GOTERM$"GO:0031975"
> > NULL
> > > GOTERM$"GO:0007067"
> > GOID = GO:0007067
> > Term = mitosis
> > Definition = The division of the eukaryotic cell nucleus to produce 
> > two daughter nuclei that, usually, contain the identical chromosome
> >      complement to their mother.
> > Ontology = BP
> > 
> > I have tried the text search methods as suggested by 
> Nianhua recently, 
> > also drew a blank.  The unifying feature of all the 
> "failures" is that 
> > they have high number GOIDs.
> > 
> > Is there a simple way of finding what the highest GOID in 
> GOstats is? 
> > Also, I guess, when might GOstats be updated!?
> > 
> > Many thanks,
> > 
> > al
> > 
> > > sessionInfo()
> > Version 2.3.1 (2006-06-01)
> > i386-pc-mingw32 
> > 
> > attached base packages:
> > [1] "splines"   "tools"     "methods"   "stats"     "graphics"
> > "grDevices" "utils"     "datasets"  "base"     
> > 
> > other attached packages:
> >    GOstats   Category   hgu95av2       KEGG   multtest genefilter
> > survival     xtable       RBGL   annotate         GO      graph
> > Ruuid    Biobase 
> >    "1.6.0"    "1.4.1"    "1.6.5"    "1.6.5"   "1.10.2"   "1.11.7"
> > "2.28"    "1.3-2"    "1.8.1"   "1.10.0"    "1.6.5"   
> "1.10.6"   "1.10.0"
> > "1.11.17" 
> >     gplots      gdata     gtools    lattice       MASS    statmod
> > sma      limma      Hmisc 
> >    "2.0.2"    "2.0.2"    "2.0.2"  "0.13-10" "7.2-27.1"    "1.2.4"
> > "0.5.15"   "2.7.10"   "3.0-12"
> > 
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> 
>